Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences.
Clicks: 101
ID: 282638
2025
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This
article has not been analysed, so there is no overall score —
reader engagement is measured and shown alongside.
Reader Engagement
Emerging Content
30.3
/100
101 views
33 readers
AI Quality Assessment
Not analyzed
Readership in this journal
EmergingRanked #117 of 121 articles by views in BMC genomics
Most read
Least read
Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 121 in total.
Mint this article as an NFT
Not yet mintedCreate a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.
5
SUSD
one-off · no wallet required
Abstract
The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences. We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time. The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.
| Reference Key |
urban2025chromosomescale
Use this key to autocite in the manuscript while using
SciMatic Manuscript Manager or Thesis Manager
|
|---|---|
| Authors | Urban, John M; Gerbi, Susan A; Spradling, Allan C |
| Journal | BMC genomics |
| Year | 2025 |
| DOI |
10.1186/s12864-025-11573-2
|
| URL | |
| Keywords |
Citations
No citations found. To add a citation, contact the admin at info@scimatic.org
Comments
No comments yet. Be the first to comment on this article.